@article{14553,
  abstract     = {Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.},
  author       = {Fedotova, Ekaterina and Kuznetsov, Nikolai and Tiunov, Egor and Ulanov, A. E. and Lvovsky, A. I.},
  issn         = {2469-9934},
  journal      = {Physical Review A},
  number       = {4},
  publisher    = {American Physical Society},
  title        = {{Continuous-variable quantum tomography of high-amplitude states}},
  doi          = {10.1103/PhysRevA.108.042430},
  volume       = {108},
  year         = {2023},
}

@article{14554,
  abstract     = {The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format.},
  author       = {Cornalba, Federico and Shardlow, Tony},
  issn         = {2804-7214},
  journal      = {ESAIM: Mathematical Modelling and Numerical Analysis},
  number       = {5},
  pages        = {3061--3090},
  publisher    = {EDP Sciences},
  title        = {{The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime}},
  doi          = {10.1051/m2an/2023077},
  volume       = {57},
  year         = {2023},
}

@article{14555,
  abstract     = {The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems.},
  author       = {Riedl, Michael and Sixt, Michael K},
  issn         = {2296-634X},
  journal      = {Frontiers in Cell and Developmental Biology},
  publisher    = {Frontiers},
  title        = {{The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction}},
  doi          = {10.3389/fcell.2023.1287420},
  volume       = {11},
  year         = {2023},
}

@article{14556,
  abstract     = {Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.},
  author       = {Berdan, Emma L. and Barton, Nicholas H and Butlin, Roger and Charlesworth, Brian and Faria, Rui and Fragata, Inês and Gilbert, Kimberly J. and Jay, Paul and Kapun, Martin and Lotterhos, Katie E. and Mérot, Claire and Durmaz Mitchell, Esra and Pascual, Marta and Peichel, Catherine L. and Rafajlović, Marina and Westram, Anja M and Schaeffer, Stephen W. and Johannesson, Kerstin and Flatt, Thomas},
  issn         = {1420-9101},
  journal      = {Journal of Evolutionary Biology},
  number       = {12},
  publisher    = {Wiley},
  title        = {{How chromosomal inversions reorient the evolutionary process}},
  doi          = {10.1111/jeb.14242},
  volume       = {36},
  year         = {2023},
}

@article{14557,
  abstract     = {Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem.},
  author       = {Dikranjan, D. and Giordano Bruno, A. and Zava, Nicolò},
  issn         = {1727-933X},
  journal      = {Quaestiones Mathematicae},
  number       = {S1},
  pages        = {191--221},
  publisher    = {Taylor & Francis},
  title        = {{Epimorphisms and closure operators of categories of semilattices}},
  doi          = {10.2989/16073606.2023.2247731},
  volume       = {46},
  year         = {2023},
}

@article{14558,
  abstract     = {n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1)  O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with  amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f
 in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m
 and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) 
 worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2
 and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds.},
  author       = {Bhattacharya, Sayan and Henzinger, Monika H and Nanongkai, Danupon and Wu, Xiaowei},
  issn         = {1095-7111},
  journal      = {SIAM Journal on Computing},
  number       = {5},
  pages        = {1132--1192},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Deterministic near-optimal approximation algorithms for dynamic set cover}},
  doi          = {10.1137/21M1428649},
  volume       = {52},
  year         = {2023},
}

@inproceedings{14559,
  abstract     = {We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.},
  author       = {Ansaripour, Matin and Chatterjee, Krishnendu and Henzinger, Thomas A and Lechner, Mathias and Zikelic, Dorde},
  booktitle    = {21st International Symposium on Automated Technology for Verification and Analysis},
  isbn         = {9783031453281},
  issn         = {1611-3349},
  location     = {Singapore, Singapore},
  pages        = {357--379},
  publisher    = {Springer Nature},
  title        = {{Learning provably stabilizing neural controllers for discrete-time stochastic systems}},
  doi          = {10.1007/978-3-031-45329-8_17},
  volume       = {14215},
  year         = {2023},
}

@misc{14562,
  abstract     = {Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.
},
  author       = {Schur, Florian KM},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning"}},
  doi          = {10.15479/AT:ISTA:14562},
  year         = {2023},
}

@article{14564,
  abstract     = {Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized.},
  author       = {Khouider, B. and GOSWAMI, BIDYUT B and Phani, R. and Majda, A. J.},
  issn         = {1942-2466},
  journal      = {Journal of Advances in Modeling Earth Systems},
  keywords     = {General Earth and Planetary Sciences, Environmental Chemistry, Global and Planetary Change},
  number       = {11},
  publisher    = {American Geophysical Union},
  title        = {{A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model}},
  doi          = {10.1029/2022ms003391},
  volume       = {15},
  year         = {2023},
}

@misc{14579,
  abstract     = {This is associated with our paper "Plant size, latitude, and phylogeny explain within-population variability in herbivory" published in Science.
},
  author       = {Wetzel, William},
  publisher    = {Zenodo},
  title        = {{HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0}},
  doi          = {10.5281/ZENODO.8133117},
  year         = {2023},
}

@phdthesis{14587,
  abstract     = {This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.
First, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.
The core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.
This thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.
In the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.
At last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.},
  author       = {Marveggio, Alice},
  issn         = {2663-337X},
  pages        = {228},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences}},
  doi          = {10.15479/at:ista:14587},
  year         = {2023},
}

@article{14603,
  abstract     = {Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.},
  author       = {Reinhardt, Aleks and Chew, Pin Yu and Cheng, Bingqing},
  issn         = {1089-7690},
  journal      = {Journal of Chemical Physics},
  number       = {18},
  publisher    = {AIP Publishing},
  title        = {{A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals}},
  doi          = {10.1063/5.0173341},
  volume       = {159},
  year         = {2023},
}

@article{14604,
  abstract     = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.},
  author       = {Toups, Melissa A and Vicoso, Beatriz},
  issn         = {1558-5646},
  journal      = {Evolution},
  number       = {11},
  pages        = {2504--2511},
  publisher    = {Oxford University Press},
  title        = {{The X chromosome of insects likely predates the origin of class Insecta}},
  doi          = {10.1093/evolut/qpad169},
  volume       = {77},
  year         = {2023},
}

@article{14605,
  abstract     = {The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments.},
  author       = {Ouyang, Niuchang and Zeng, Zezhu and Wang, Chen and Wang, Qi and Chen, Yue},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {17},
  publisher    = {American Physical Society},
  title        = {{Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)}},
  doi          = {10.1103/PhysRevB.108.174302},
  volume       = {108},
  year         = {2023},
}

@inproceedings{14609,
  abstract     = {Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The
core ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art.},
  author       = {Das, Sourav and Xiang, Zhuolun and Kokoris Kogias, Eleftherios and Ren, Ling},
  booktitle    = {32nd USENIX Security Symposium},
  isbn         = {9781713879497},
  location     = {Anaheim, CA, United States},
  pages        = {5359--5376},
  publisher    = {Usenix},
  title        = {{Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling}},
  volume       = {8},
  year         = {2023},
}

@article{14610,
  abstract     = {Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host.},
  author       = {Bussi, Claudio and Mangiarotti, Agustín and Vanhille-Campos, Christian Eduardo and Aylan, Beren and Pellegrino, Enrica and Athanasiadi, Natalia and Fearns, Antony and Rodgers, Angela and Franzmann, Titus M. and Šarić, Anđela and Dimova, Rumiana and Gutierrez, Maximiliano G.},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {1062--1069},
  publisher    = {Springer Nature},
  title        = {{Stress granules plug and stabilize damaged endolysosomal membranes}},
  doi          = {10.1038/s41586-023-06726-w},
  volume       = {623},
  year         = {2023},
}

@misc{14614,
  abstract     = {Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.},
  author       = {Lasne, Clementine and Elkrewi, Marwan N},
  keywords     = {Panorpa, scorpionfly, genome, transcriptome},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome}},
  doi          = {10.15479/AT:ISTA:14614},
  year         = {2023},
}

@misc{14616,
  abstract     = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.},
  author       = {Toups, Melissa A and Vicoso, Beatriz},
  publisher    = {Dryad},
  title        = {{The X chromosome of insects likely predates the origin of Class Insecta}},
  doi          = {10.5061/DRYAD.HX3FFBGKT},
  year         = {2023},
}

@misc{14617,
  abstract     = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.},
  author       = {Toups, Melissa A and Vicoso, Beatriz},
  publisher    = {Zenodo},
  title        = {{The X chromosome of insects likely predates the origin of Class Insecta}},
  doi          = {10.5281/ZENODO.8138705},
  year         = {2023},
}

@misc{14619,
  abstract     = {Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).},
  author       = {Cheng, Bingqing},
  publisher    = {Zenodo},
  title        = {{BingqingCheng/solubility: V1.0}},
  doi          = {10.5281/ZENODO.8398094},
  year         = {2023},
}